[Biopython] Using Tabix on a bgzf file

Vishnu Chilakamarri vishnuc11j93 at gmail.com
Sun Feb 16 03:39:58 UTC 2014


Hi Peter,

I read your code on bgzf compression and the blog post. I used
uniprot_sprot_varsplic.fasta.gz<ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot_varsplic.fasta.gz>as
the example (from the EBI ftp) to compress in bgzf and then index
using
Tabix. Now the file I've gotten has a .tbi extension. I'm trying to parse
the file but gives a preset not provided error and when I'm trying to
access columns I'm getting indexes overlap error. Can you tell me where
I've gone wrong?

Thank you,
Vishnu



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